The article uses alleged remarks made by Her Royal Highness to pro-EU Nick Clegg during a lunch at Windsor Castle when he was Deputy Prime Minister back in 2011, in which she said the EU was heading in the wrong direction.
A "highly reliable senior source" told The Sun: "People who heard their conversation were left in no doubt at all about the Queen’s views on European integration.
"It was really something, and it went on for quite a while. The EU is clearly something Her Majesty feels passionately about," the source was quoted as saying.
Another incident in which she reportedly she "doesn't understand Europe" is also described.
Buckingham Palace have been quick to respond to the claims reiterating the "Queen remains politically neutral as she has for 63 years" and calling the story "spurious".
Clegg was more forthright in his criticism, calling the story "nonsense":
A spokesman later added: "This is categorically untrue. Nick has no recollection of this conversation and it is not the sort of conversation you forget."
Despite the alleged incident occurring well before David Cameron announced the Brexit referendum, Eurosceptics jumped on the story as evidence "a boost" for the campaign to leave the EU.
Others however suspect the "threadbare" story is simply the Murdoch-owned tabloid pursuing its own anti-EU agenda.
Even The Sun's own picture captions seemed doubtful.
While the BBC's Andrew Marr seemed in two minds:
Whatever was actually said at Windsor Castle that day, attention has now turned to who the "highly reliable senior source" could be, with many quick to point out that cabinet member and prominent Brexiter Michael Gove was among those attending the event:
Despite her official position of being politically neutral, the Queen has been drawn into political debates with her comments before, most noticeably in the run-up to the Scottish Independence referendum.
She reportedly said she hoped people will "think very carefully about the future" as the Scottish independence referendum campaign entered its final days in September 2014.